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Method: A virome-wide clonal integration analysis platform for discovering cancer viral etiology
- Xun Chen,
- Jason Kost,
- Arvis Sulovari,
- Nathalie Wong,
- Winnie S. Liang,
- Jian Cao,
- and Dawei Li
Genome Res. May 2019 29: 819-830; Published in Advance March 14, 2019, doi:10.1101/gr.242529.118
.... Oncoviral profiles can be obtained from cancer sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early...
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Method: Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing
- Brigid M. O'Flaherty,
- Yan Li,
- Ying Tao,
- Clinton R. Paden,
- Krista Queen,
- Jing Zhang,
- Darrell L. Dinwiddie,
- Stephen M. Gross,
- Gary P. Schroth,
- and Suxiang Tong
Genome Res. June 2018 28: 869-877; Published in Advance April 27, 2018, doi:10.1101/gr.226316.117
...target sequence reads and improved depth of coverage.Sequence-specific enrichment probes have also been used in the study of the human virome (Briese et al. 2015; Wylie et al. 2015). Briese and colleagues developed the Virome Capture Sequencing Platform for vertebrate viruses, where the authors designed...
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Research: The human gut virome: Inter-individual variation and dynamic response to diet
- Samuel Minot,
- Rohini Sinha,
- Jun Chen,
- Hongzhe Li,
- Sue A. Keilbaugh,
- Gary D. Wu,
- James D. Lewis,
- and Frederic D. Bushman
Genome Res. October 2011 21: 1616-1625; Published in Advance August 31, 2011, doi:10.1101/gr.122705.111
...requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...of the specimen, we anticipated a significant fragmentation in the historical RNA sequences possibly present within the tissue matrix. Therefore, we used an RNA extraction protocol targeting small RNA molecules, specifically designed for miRNA sequencing, on each of the six tissue samples obtained (see Methods...
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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
...enhanced with Hi-C information and longer reads sequencing to connect scaffolds into chromosomal assembles (Dudchenko et al. 2017; Matthews et al. 2018; Palatini et al. 2020). From these assemblies, the transposon consensus sequences list were processed to reduce redundancy (Supplemental Fig. S1...
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Research: Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci
- Ted Hong,
- Sreeja Parameswaran,
- Omer A. Donmez,
- Daniel Miller,
- Carmy Forney,
- Michael Lape,
- Mariana Saint Just Ribeiro,
- Jun Liang,
- Lee E. Edsall,
- Albert F. Magnusen,
- William Miller,
- Iouri Chepelev,
- John B. Harley,
- Bo Zhao,
- Leah C. Kottyan,
- and Matthew T. Weirauch
Genome Res. December 2021 31: 2185-2198; Published in Advance November 19, 2021, doi:10.1101/gr.264705.120
...) in the etiology of human disease (Lee and Young 2013; Deplancke et al. 2016). Regulatory proteins bind to promoter regions and distal regions of target genes (e.g., enhancers) to alter gene expression through numerous mechanisms (for reviews, see Lambert et al. 2018; Sullivan et al. 2018; Schoenfelder and Fraser...
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...-suggested protocol. cDNA was synthesized using the SuperScript VILO cDNA Synthesis Kit (Cat# 11754-050, Life technologies). RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (Cat# KK8421, Kapa Biosystems) and sequenced on an Illumina HiSeq. To remove batch effects, matched...
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Resource: The NIH Human Microbiome Project
- The NIH HMP Working Group,
- Jane Peterson,
- Susan Garges,
- Maria Giovanni,
- Pamela McInnes,
- Lu Wang,
- Jeffery A. Schloss,
- Vivien Bonazzi,
- Jean E. McEwen,
- Kris A. Wetterstrand,
- Carolyn Deal,
- Carl C. Baker,
- Valentina Di Francesco,
- T. Kevin Howcroft,
- Robert W. Karp,
- R. Dwayne Lunsford,
- Christopher R. Wellington,
- Tsegahiwot Belachew,
- Michael Wright,
- Christina Giblin,
- Hagit David,
- Melody Mills,
- Rachelle Salomon,
- Christopher Mullins,
- Beena Akolkar,
- Lisa Begg,
- Cindy Davis,
- Lindsey Grandison,
- Michael Humble,
- Jag Khalsa,
- A. Roger Little,
- Hannah Peavy,
- Carol Pontzer,
- Matthew Portnoy,
- Michael H. Sayre,
- Pamela Starke-Reed,
- Samir Zakhari,
- Jennifer Read,
- Bracie Watson,
- and Mark Guyer
Genome Res. December 2009 19: 2317-2323; Published in Advance October 9, 2009, doi:10.1101/gr.096651.109
...at the four major sites of microbial colonization in the human body: mouth, gut, vagina, and skin.’’ Relman (2002) envisioned that the ‘‘characterization of themicrobiomewould be accomplished through random shotgun sequencing procedures, targeted large-insert clone sequencing, and assessments of intra...
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